Globin-coupled sensors, protoglobins, and the last universal common ancestor
Section snippets
History
In February of 2000, the first heme-based aerotactic transducers (HemAT) in Archaea and Bacteria were discovered [1]. Identified initially by their absorption spectra and heme-staining, HemAT-Hs from Halobacterium salinarum and HemAT-Bs from Bacillus subtilis were shown by time-lapsed capillary assay [2] to elicit aerophobic and aerophilic responses, respectively. While their C-termini were clearly identified as signaling domains analogous to those of bacterial chemotaxis proteins (MCP), the
Background
Globins are ubiquitous heme-binding α-helical proteins whose function is principally thought to regulate oxygen homoeostasis [1], [9]. Initially described as an eight-helix globin fold labeled A through H [10], other members of the globin family have been observed that are less helical, with the “truncated” globins maintaining the overall globin fold with as few as four helices [11]. In contrast to PAS domains that can bind an assortment of cofactors, globins are known to bind only heme.
The
GCS functional classification
As the number and domain variability of the GCSs identified increased, it became increasingly difficult to classify them on their own. Hence, all biological heme-based sensors with known functions were collected and classified as either aerotactic or gene regulating [7]. The gene regulating group was further subdivided into three subgroups: protein–DNA [23], [24], [25], [26], [27], protein–protein [1], [28], [29], [30], and second messenger [31], [32], [33], [34], [35], [36] pathways. The
GCS diversity and evolution
Examination of the GCS phylogenetic tree presented in Fig. 1(b) results in two possible interpretations: (1) certain bacterial species have a preference for specific signal transducing elements, and/or (2) the globin domains have evolved simultaneously with their signal transducing partners. Since the tree created was based on the globin sensor domain only, the branching-by-function observed demonstrates that aerotactic-type globins evolved from a common ancestral globin, or protoglobin, as did
Protoglobins in the archaea
Four proteins have been identified that conform to the protoglobin criteria set forth above, however only the archaeal proteins have been further analyzed [8]. These proteins were identified in the genome sequences of the Actinobacterium Thermobifida fusca, the green non-sulfur bacterium Chloroflexus aurantiacus, and the two Archaea A. pernix and M. acetivorans.
The proximal histidine was initially identified by sequence analysis (Fig. 1(a)) and later confirmed in the Archaeal protoglobins by
Ancient oxygen signaling and the future
The globin fold is successful at protecting the heme iron from rapid oxidation and yet allows reversible O2 binding. PAS domains are capable of accepting various input stimuli and participate in proteins regulating a whole slew of functions [40]. Some PAS domains are heme-binding (heme-PAS) domains as well, also capable of reversibly binding oxygen. A computer simulation study based on known PAS structures [52] suggests that a common conformational flexibility exists between these structures
Acknowledgement
This investigation was supported by a National Science Foundation Grant MCB0080125 and by a University of Hawaii intramural grant (M.A.).
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